In recent years, fuel cell systems have been developed which have as an energy source a fuel cell that generates electric power through an electrochemical reaction of a reaction gas (fuel gas and oxidant gas). This type of fuel cell system may be configured to cool the fuel cell while the operation is stopped more rapidly than during normal operation and delay the deteriorative reaction of the fuel gas due to carbon oxidation caused by gas remaining in the fuel cell (see, for example, Patent Document 1), or may be configured to allow the fuel cell to circulate the cooling water until the temperature of the fuel cell, after the power generation is stopped, is below the cooling water circulation stop temperature which is the criterion of judgment for stopping the circulation of the cooling water (see, for example, Patent Document 2).